update report, sort version issues. rebase after this

Author: nschan

assets/report/functions/read_busco.R

@@ -75,6 +75,7 @@ read_busco_batch <- \(x) {read_tsv(x, show_col_types = F) %>%
         str_detect(x, "pilon") ~ "pilon",
         str_detect(x, "longstitch") ~ "longstitch",
         str_detect(x, "links") ~ "LINKS",
+        str_detect(x, "yahs") ~ "HiC",
         str_detect(x, "assembl[ey]") ~ "Assembly",
       ),
       Percent_gaps = Percent_gaps %>% str_remove("%") %>% as.numeric) %>%

assets/report/scripts/_busco_page.R

@@ -11,7 +11,7 @@ for (i in 1:length(unique(busco_reports$group))) {
       dplyr::select(sample, stage, Var, value) |>
       mutate(Var = str_replace_all(Var, "_", " ") |> str_replace_all("percent", "(%)")) |>
       pivot_wider(names_from = "Var", values_from = "value", id_cols = c(sample,stage)) |>
-      dplyr::arrange(factor(stage, levels = c("Assembly","medaka", "pilon", "dorado","links","longstitch","ragtag")), sample) |>
+      dplyr::arrange(factor(stage, levels = c("Assembly","medaka", "pilon", "dorado","hic","links","longstitch","ragtag")), sample) |>
       gt::gt() |>
       gt::fmt_auto() |>
       gt::opt_stylize(color = "gray") |>

assets/report/scripts/_merqury.R

@@ -13,6 +13,7 @@ merqury_stats <- list.files(paste0(data_base, "merqury"), full.names = T, patter
           str_detect(x, "_pilon") ~ "pilon",
           str_detect(x, "_longstitch") ~ "longstitch",
           str_detect(x, "_links") ~ "LINKS",
+          str_detect(x, "_yahs") ~ "HiC",
           str_detect(x, "assembl[ey]") ~ "Assembly",
           TRUE ~ "Unknown")) }) |>
   bind_rows() |>

assets/report/scripts/_quast.R

@@ -18,10 +18,11 @@ quast_stats <- list.files(paste0(data_base, "quast"),
           str_detect(x, "_pilon") ~ "pilon",
           str_detect(x, "_longstitch") ~ "longstitch",
           str_detect(x, "_links") ~ "LINKS",
+          str_detect(x, "_yahs") ~ "HiC",
           str_detect(x, "assembl[ey]") ~ "Assembly",
           TRUE ~ "Unknown")) }) |>
   left_join(groups, by = join_by(sample)) |>
-  mutate(stage = stage |> fct_relevel("Assembly", "medaka", "pilon", "longstitch", "LINKS", "RagTag") ) |>
+  mutate(stage = stage |> fct_relevel("Assembly", "medaka", "dorado", "pilon", "longstitch", "LINKS", "HiC", "RagTag") ) |>
   dplyr::arrange(sample, stage)
 
 # This creates code that will generate the length plot based on the contents of the quast report.

conf/modules/QC/busco.config

@@ -55,7 +55,7 @@ process {
         ]
     }
     withName: '.*:SCAFFOLD:.*HIC:QC.*:BUSCO' {
-        ext.prefix = { "${meta.id}_hic-${lineage}" }
+        ext.prefix = { "${meta.id}_yahs-${lineage}" }
         publishDir = [
             path: { "${params.outdir}/${meta.id}/QC/BUSCO/" },
             mode: params.publish_dir_mode,

conf/modules/QC/merqury.config

@@ -40,7 +40,7 @@ process {
         ]
     }
     withName: '.*:SCAFFOLD:HIC:.*:MERQURY' {
-        ext.prefix = { "${meta.id}_hic" }
+        ext.prefix = { "${meta.id}_yahs" }
         publishDir = [
             path: { "${params.outdir}/${meta.id}/QC/merqury/" },
             mode: params.publish_dir_mode,

conf/modules/QC/quast.config

@@ -40,7 +40,7 @@ process {
         ]
     }
     withName: '.*SCAFFOLD:HIC.*:QUAST' {
-        ext.prefix = { "${meta.id}_hic" }
+        ext.prefix = { "${meta.id}_yahs" }
         publishDir = [
             path: { "${params.outdir}/${meta.id}/QC/QUAST/" },
             mode: params.publish_dir_mode,

subworkflows/local/scaffolding/main.nf

@@ -172,33 +172,39 @@ workflow SCAFFOLD {
     RUN_LINKS.out.busco_out.set { links_busco }
     RUN_LINKS.out.quast_out.set { links_quast }
     RUN_LINKS.out.merqury_report_files.set { links_merqury }
-
     ch_versions = ch_versions.mix(RUN_LINKS.out.versions)
 
     RUN_LONGSTITCH.out.busco_out.set { longstitch_busco }
     RUN_LONGSTITCH.out.quast_out.set { longstitch_quast }
     RUN_LONGSTITCH.out.merqury_report_files.set { longstitch_merqury }
     ch_versions = ch_versions.mix(RUN_LONGSTITCH.out.versions)
 
+    HIC.out.busco_out.set { hic_busco }
+    HIC.out.quast_out.set { hic_quast }
+    HIC.out.merqury_report_files.set { hic_merqury }
+    ch_versions = ch_versions.mix(HIC.out.versions)
+
     RUN_RAGTAG.out.busco_out.set { ragtag_busco }
     RUN_RAGTAG.out.quast_out.set { ragtag_quast }
     RUN_RAGTAG.out.merqury_report_files.set { ragtag_merqury }
-
     ch_versions = ch_versions.mix(RUN_RAGTAG.out.versions)
 
     links_busco
         .concat(longstitch_busco)
         .concat(ragtag_busco)
+        .concat(hic_busco)
         .set { scaffold_busco_reports }
 
     links_quast
         .concat(longstitch_quast)
         .concat(ragtag_quast)
+        .concat(hic_quast)
         .set { scaffold_quast_reports }
 
     links_merqury
         .concat(longstitch_merqury)
         .concat(ragtag_merqury)
+        .concat(hic_merqury)
         .set { scaffold_merqury_reports }
 
     versions = ch_versions